PING 2.2.0
Renan Sauteraud
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/PING | | Last Changed Rev: 74040 / Revision: 74773 | | Last Changed Date: 2013-03-07 14:51:53 -0800 (Thu, 07 Mar 2013) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/PING.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PING/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PING’ version ‘2.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘PING’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 51.2Mb
sub-directories of 1Mb or more:
extdata 50.0Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file(s) in a non-standard place:
src/inst/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
‘/loc/home/biocbuild/bbs-2.11-bioc/meat/PING.Rcheck/00check.log’
for details.
* installing *source* package ‘PING’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ping.c -o ping.o
ping.c: In function ‘fitModelAllk’:
ping.c:145:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
ping.c: In function ‘iterEM’:
ping.c:659:25: warning: unused variable ‘mu’ [-Wunused-variable]
ping.c: In function ‘ECM1’:
ping.c:912:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
ping.c:1072:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
ping.c:760:15: warning: unused variable ‘k’ [-Wunused-variable]
ping.c: In function ‘ECM1PE’:
ping.c:1320:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
ping.c:1473:3: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
ping.c:1108:15: warning: unused variable ‘k’ [-Wunused-variable]
ping.c: In function ‘ECM2’:
ping.c:1536:66: warning: unused variable ‘ee’ [-Wunused-variable]
ping.c:1536:57: warning: unused variable ‘ggR’ [-Wunused-variable]
ping.c:1536:52: warning: unused variable ‘ggF’ [-Wunused-variable]
ping.c:1536:47: warning: unused variable ‘aaR’ [-Wunused-variable]
ping.c:1536:42: warning: unused variable ‘aaF’ [-Wunused-variable]
ping.c:1536:29: warning: unused variable ‘etaDiff’ [-Wunused-variable]
ping.c:1536:9: warning: variable ‘chiSum’ set but not used [-Wunused-but-set-variable]
ping.c:1527:15: warning: unused variable ‘k’ [-Wunused-variable]
ping.c: In function ‘ECM2PE’:
ping.c:1743:66: warning: unused variable ‘ee’ [-Wunused-variable]
ping.c:1743:57: warning: unused variable ‘ggR’ [-Wunused-variable]
ping.c:1743:52: warning: unused variable ‘ggF’ [-Wunused-variable]
ping.c:1743:47: warning: unused variable ‘aaR’ [-Wunused-variable]
ping.c:1743:42: warning: unused variable ‘aaF’ [-Wunused-variable]
ping.c:1743:29: warning: unused variable ‘etaDiff’ [-Wunused-variable]
ping.c:1734:15: warning: unused variable ‘k’ [-Wunused-variable]
ping.c: In function ‘getInfMat’:
ping.c:2590:80: warning: unused variable ‘PhiRw’ [-Wunused-variable]
ping.c:2590:73: warning: unused variable ‘PhiFw’ [-Wunused-variable]
ping.c: In function ‘getInfMatPE’:
ping.c:3040:59: warning: unused variable ‘PhiFRw’ [-Wunused-variable]
ping.c: In function ‘mergePeak’:
ping.c:3312:20: warning: variable ‘tstatMax’ set but not used [-Wunused-but-set-variable]
ping.c:3301:11: warning: unused variable ‘j’ [-Wunused-variable]
ping.c:3301:7: warning: unused variable ‘i’ [-Wunused-variable]
ping.c: In function ‘BIC’:
ping.c:2101:6: warning: ‘penalty’ may be used uninitialized in this function [-Wuninitialized]
ping.c: In function ‘BICPE’:
ping.c:2208:6: warning: ‘penalty’ may be used uninitialized in this function [-Wuninitialized]
ping.c: In function ‘fitModelK’:
ping.c:477:18: warning: ‘firstFit’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/usr/local/lib64 -o PING.so init.o ping.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/PING.Rcheck/PING/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘PING’
** help
*** installing help indices
** building package indices
** installing vignettes
‘PING-PE.Rnw’
‘PING.Rnw’
** testing if installed package can be loaded
* DONE (PING)